rs941389

Variant names:

• chr4-69496023-A-C
• rs941389
• ENST00000968901.1:c.-42-120T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-69496023-A-C
• chr4-69496023-A-G
• chr4-69496023-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001297616.2(UGT2B4):​c.44-613T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 1,237,918 control chromosomes in the GnomAD database, including 80,331 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.34 (8720 hom., cov: 32)
  • Exomes 𝑓: 0.36 (71611 hom.)
• Consequence: UGT2B4 NM_001297616.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 6 publications found

Genes affected

UGT2B4 (HGNC:12553): (UDP glucuronosyltransferase family 2 member B4) Enables glucuronosyltransferase activity. Involved in cellular glucuronidation and estrogen metabolic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001297616.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B4	NM_001297616.2		c.44-613T>G		intron	N/A	NP_001284545.1
	UGT2B4	NM_021139.3	MANE Select	c.-162T>G		upstream_gene	N/A	NP_066962.2
	UGT2B4	NM_001297615.2		c.-162T>G		upstream_gene	N/A	NP_001284544.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B4	ENST00000968901.1		c.-42-120T>G		intron	N/A	ENSP00000638960.1
	UGT2B4	ENST00000510114.1	TSL:4	c.-105-57T>G		intron	N/A	ENSP00000421113.1
	UGT2B4	ENST00000502655.5	TSL:5	n.329-613T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51159 AN: 151888 Hom.: 8724 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.340

GnomAD4 exome AF: 0.359 AC: 390201 AN: 1085912 Hom.: 71611 AF XY: 0.359 AC XY: 191799 AN XY: 533812

African (AFR) AF: 0.298 AC: 7098 AN: 23812

American (AMR) AF: 0.291 AC: 5810 AN: 19948

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 5825 AN: 17034

East Asian (EAS) AF: 0.221 AC: 7481 AN: 33786

South Asian (SAS) AF: 0.365 AC: 17371 AN: 47568

European-Finnish (FIN) AF: 0.320 AC: 10539 AN: 32978

Middle Eastern (MID) AF: 0.342 AC: 1603 AN: 4690

European-Non Finnish (NFE) AF: 0.370 AC: 318351 AN: 859840

Other (OTH) AF: 0.349 AC: 16123 AN: 46256

GnomAD4 genome AF: 0.337 AC: 51175 AN: 152006 Hom.: 8720 Cov.: 32 AF XY: 0.332 AC XY: 24680 AN XY: 74290

African (AFR) AF: 0.295 AC: 12245 AN: 41472

American (AMR) AF: 0.311 AC: 4739 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1195 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1335 AN: 5168

South Asian (SAS) AF: 0.362 AC: 1747 AN: 4826

European-Finnish (FIN) AF: 0.324 AC: 3417 AN: 10558

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25368 AN: 67936

Other (OTH) AF: 0.340 AC: 719 AN: 2114

Alfa AF: 0.345 Hom.: 2847

Bravo AF: 0.333

Asia WGS AF: 0.314 AC: 1085 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.23
DANN	Benign	0.39
PhyloP100		-0.41
PromoterAI		-0.040	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs941389; hg19: chr4-70361741; COSMIC: COSV59315927;